Reproductive & Developmental Biology Laboratory, Research Triangle Park, NC 27709, USA.
Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
Nucleic Acids Res. 2024 Oct 14;52(18):10897-10917. doi: 10.1093/nar/gkae714.
Chromatin changes in response to estrogen and progesterone are well established in cultured cells, but how they control gene expression under physiological conditions is largely unknown. To address this question, we examined in vivo estrous cycle dynamics of mouse uterus hormone receptor occupancy, chromatin accessibility and chromatin structure by combining RNA-seq, ATAC-seq, HiC-seq and ChIP-seq. Two estrous cycle stages were chosen for these analyses, diestrus (highest estrogen) and estrus (highest progesterone). Unexpectedly, rather than alternating with each other, estrogen receptor alpha (ERα) and progesterone receptor (PGR) were co-bound during diestrus and lost during estrus. Motif analysis of open chromatin followed by hypoxia inducible factor 2A (HIF2A) ChIP-seq and conditional uterine deletion of this transcription factor revealed a novel role for HIF2A in regulating diestrus gene expression patterns that were independent of either ERα or PGR binding. Proteins in complex with ERα included PGR and cohesin, only during diestrus. Combined with HiC-seq analyses, we demonstrate that complex chromatin architecture changes including enhancer switching are coordinated with ERα and PGR co-binding during diestrus and non-hormone receptor transcription factors such as HIF2A during estrus to regulate most differential gene expression across the estrous cycle.
染色质在雌激素和孕激素的作用下发生变化在培养细胞中已得到充分证实，但它们在生理条件下如何控制基因表达在很大程度上仍是未知的。为了解决这个问题，我们通过结合 RNA-seq、ATAC-seq、HiC-seq 和 ChIP-seq，研究了体内动情周期中小鼠子宫中激素受体占据、染色质可及性和染色质结构的动态变化。选择了两个动情周期阶段进行这些分析，即发情前期（雌激素最高）和发情期（孕激素最高）。出乎意料的是，雌激素受体 alpha（ERα）和孕激素受体（PGR）在发情前期并没有相互交替结合，而是在发情期失去结合。对开放染色质进行基序分析，然后进行缺氧诱导因子 2A（HIF2A）ChIP-seq，以及对该转录因子进行条件性子宫缺失，揭示了 HIF2A 在调节发情前期基因表达模式方面的一个新作用，这与 ERα 或 PGR 结合无关。与 ERα 结合的蛋白包括 PGR 和黏连蛋白，仅在发情前期存在。结合 HiC-seq 分析，我们证明了复杂的染色质结构变化，包括增强子切换，与 ERα 和 PGR 共结合在发情前期协调发生，而在发情期则与非激素受体转录因子如 HIF2A 协调发生，以调节整个动情周期中大多数差异基因的表达。
